Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation

Abstract

Background: Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of these metabolic and underlying regulatory processes allow a detailed understanding of carbon distribution within the plant and the formation of associated phenotypic traits. Sucrose translocation from 'source' tissues (e.g. mesophyll) to 'sink' tissues (e.g. root) is tightly bound to the proton gradient across the membranes. The plant sucrose transporters are grouped into efflux exporters (SWEET family) and proton-symport importers (SUC, STP families). To better understand regulation of sucrose export from source tissues and sucrose import into sink tissues, there is a need for a metabolic model that takes in account the tissue organisation of Arabidopsis thaliana with corresponding metabolic specificities of respective tissues in terms of sucrose and proton production/utilization. An ability of the model to operate under different light modes ('light' and 'dark') and correspondingly in different energy producing modes is particularly important in understanding regulatory modules.

Results: Here, we describe a multi-compartmental model consisting of a mesophyll cell with plastid and mitochondrion, a phloem cell, as well as a root cell with mitochondrion. In this model, the phloem was considered as a non-growing transport compartment, the mesophyll compartment was considered as both autotrophic (growing on CO₂ under light) and heterotrophic (growing on starch in darkness), and the root was always considered as heterotrophic tissue dependent on sucrose supply from the mesophyll compartment. In total, the model includes 413 balanced compounds interconnected by 400 transformers. The structured metabolic model accounts for central carbon metabolism, photosynthesis, photorespiration, carbohydrate metabolism, energy and redox metabolisms, proton metabolism, biomass growth, nutrients uptake, proton gradient generation and sucrose translocation between tissues. Biochemical processes in the model were associated with gene-products (742 ORFs). Flux Balance Analysis (FBA) of the model resulted in balanced carbon, nitrogen, proton, energy and redox states under both light and dark conditions. The main H⁺-fluxes were reconstructed and their directions matched with proton-dependent sucrose translocation from 'source' to 'sink' under any light condition.

Conclusions: The model quantified the translocation of sucrose between plant tissues in association with an integral balance of protons, which in turn is defined by operational modes of the energy metabolism.

Keywords: Central carbon metabolism; Diurnal growth; Energy metabolism; Flux balance analysis; Multi-compartment metabolic model; Sucrose metabolism; Sucrose transport.

Fig. 1

Expression of sucrose transporter genes in different tissues of Arabidopsis thaliana. Overview of the sucrose transporter families SWEET (sucrose efflux transporters), SUC and STP (sucrose-proton symporters). The image of Arabidopsis has been adopted from [83]

Fig. 2

Expression of sucrose transporter genes in Arabidopsis thaliana in leaves and roots during development. Absolute intensity values of sucrose transporter genes expression in leaves and roots during development (7–35 days). SWEET efflux-transporters and SUC/STP influx-transporters are both highly expressed in leaf while the root mainly expresses SUC/STP influx-transporters. The plot is based on gcRMA normalized data selected from [84] based on TAIR ExpressionSet 1007966126 [85]

Fig. 3

Simplified mechanism of sucrose translocation from autotrophic to heterotrophic tissues via connecting tissue. The autotrophic tissue (mesophyll) synthesises sucrose that is translocated to heterotrophic tissue (root) as carbon and energy source to build biomass. Metabolically active tissues form a proton gradient with the extracellular space (apoplast), which is used by the sink tissue to uptake sucrose. suc – sucrose, H ⁺ – proton, SWEET – sucrose efflux transporters, SUC,STP – sucrose-proton symporters. Size of letters represents relative concentrations

Fig. 4

Schematic circuit of the central carbon and energy metabolisms of Arabidopsis thaliana. The model consists of super-compartment ‘plant’, which includes growing autotrophic sub-compartment ‘mesophyll’, non-growing transport sub-compartment ‘phloem’ and growing heterotrophic sub-compartment ‘root’. The inner space of the super-compartment ‘plant’ was defined as of ‘apoplast’. The ‘mesophyll’ compartment contained ‘plastid’ and ‘mitochondrion’ while the ‘root’ compartment only contained ‘mitochondrion’. Details of metabolic pathways were hidden in order to focus only on the specificity of the sucrose synthesis/translocation in relation of H⁺-turnover, nutrient and water transport between tissues. hv – light photon; GAP – glyceraldehyde 3-phosphate; suc – sucrose; g6p – glucose-6-phosphate; f6p – fructose-6-phosphate; oaa – oxaloacetate; mal – malate; H ⁺ – proton; ETC. – electron transport chain, that performs oxidative phosphorylation; growth – collective set of reactions resulted in formation of biomass; ATPsunt. – ATP synthase; nutrient – nutrients such as NO ₃⁻, HPO ₄^2 −, SO ₄²⁻, SWEET – sucrose efflux transporters, SUC,STP – sucrose-proton symporters

Fig. 5

Generalized view on functioning of the malate/oxaloacetate shuttle in the mesophyll. The depicted metabolic scenario was elaborated based on the Flux Balance Analysis. PS – photosynthesis system; PPP – pentose-phosphate pathway; CBC – Calvin-Benson cycle; NADPH-MDH –NADPH-dependent malate dehydrogenase, which is marked as light sensitive; OAA – oxaloacetate; OxPhos – oxidative phosphorylation; ATP/ADP translocator is bidirectional in plastid and unidirectional in mitochondrion

Fig. 6

Relationship between translocated fractions of ATP and NADPH within their total balance in the plastid under light conditions. Fractions of ATP or NADPH that are exchanged between plastid and cytosol through ATP/ADP translocator (T.ATP) and malate/oxaloacetate shuttle (T.NADPH) depend on the FQR/FNR ratio (the ratio between cyclic [FQR] and non-cyclic [FNR] electron flow through photosynthesis light reactions). Cyclic electron flow through photosynthesis light reactions increases ATP yield without corresponding increase in NADPH formation. This estimate was done under assumption of fixed flux ratio photorespiration / photosynthesis = 0.25. Positive values of T.ATP/ATP indicate import of ATP to the plastid from cytosol, zero value indicate self-sufficient ATP balance in the plastid, while the negative values points on ATP export to cytosol. Negative values of T.NADPH/NADPH indicate export reduced equivalents from plastid via malate/oxaloacetate shuttle, while zero values indicate self-sufficient NADPH balance in the plastid. The shaded area, an ATP/NADPH ratio of 1.3 - 1.5 indicates the ratio required to ensure CO₂-fixation in the Calvin-Benson-Cycle [63, 73]

Fig. 7

Proton balance in relation with sucrose translocation and growth conditions. The proton balance was predicted by FBA in all three compartments of the model: mesophyll, phloem and root. The presented ‘light’ conditions are: photorespiration/photosynthesis = 0.25 and FQR/FNR = 0.37. Under these constraints the ATP balance in plastid is predicted to be self-sufficient (Fig. 6), therefore there was no ATP and H⁺ exchange between plastid and cytosol. The contribution of major H⁺-producing/consuming processes into overall proton balance in each compartment was summarized and denoted as percentages of contribution. Different shapes and colours of the nodes represent the different pools of protons. The proton turnovers in each compartment were normalized per cytoplasm of root, since it was almost invariant under both light conditions. The ‘root’ compartment exchanged protons with the environment, which were acquired in symport with the nutrients and excreted via H⁺/ATPase. N – nutrients